1
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Kurkowiak M, Grasso G, Faktor J, Scheiblecker L, Winniczuk M, Mayordomo MY, O'Neill JR, Oster B, Vojtesek B, Al-Saadi A, Marek-Trzonkowska N, Hupp TR. An integrated DNA and RNA variant detector identifies a highly conserved three base exon in the MAP4K5 kinase locus. RNA Biol 2021; 18:2556-2575. [PMID: 34190025 PMCID: PMC8632122 DOI: 10.1080/15476286.2021.1932345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
RNA variants that emerge from editing and alternative splicing form important regulatory stages in protein signalling. In this report, we apply an integrated DNA and RNA variant detection workbench to define the range of RNA variants that deviate from the reference genome in a human melanoma cell model. The RNA variants can be grouped into (i) classic ADAR-like or APOBEC-like RNA editing events and (ii) multiple-nucleotide variants (MNVs) including three and six base pair in-frame non-canonical unmapped exons. We focus on validating representative genes of these classes. First, clustered non-synonymous RNA edits (A-I) in the CDK13 gene were validated by Sanger sequencing to confirm the integrity of the RNA variant detection workbench. Second, a highly conserved RNA variant in the MAP4K5 gene was detected that results most likely from the splicing of a non-canonical three-base exon. The two RNA variants produced from the MAP4K5 locus deviate from the genomic reference sequence and produce V569E or V569del isoform variants. Low doses of splicing inhibitors demonstrated that the MAP4K5-V569E variant emerges from an SF3B1-dependent splicing event. Mass spectrometry of the recombinant SBP-tagged MAP4K5V569E and MAP4K5V569del proteins pull-downs in transfected cell systems was used to identify the protein-protein interactions of these two MAP4K5 isoforms and propose possible functions. Together these data highlight the utility of this integrated DNA and RNA variant detection platform to detect RNA variants in cancer cells and support future analysis of RNA variant detection in cancer tissue.
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Affiliation(s)
- Małgorzata Kurkowiak
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland
| | - Giuseppa Grasso
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland.,Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Lisa Scheiblecker
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Małgorzata Winniczuk
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland
| | - Marcos Yebenes Mayordomo
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland.,University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
| | - J Robert O'Neill
- Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Bodil Oster
- QIAGEN Aarhus, Silkeborgvej 2, 8000 Aarhus, Denmark
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ali Al-Saadi
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland.,Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Ted R Hupp
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland.,University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
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2
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Suzuki H, Matsuoka M. Proline-arginine poly-dipeptide encoded by the C9orf72 repeat expansion inhibits adenosine deaminase acting on RNA. J Neurochem 2021; 158:753-765. [PMID: 34081786 DOI: 10.1111/jnc.15445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022]
Abstract
A GGGGCC hexanucleotide repeat expansion in the C9orf72 gene is linked to the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9-ALS/FTD). Unconventional translation of the hexanucleotide repeat expansion generates five dipeptide repeat proteins (DPRs). The molecular mechanism underlying the DPR-linked neurotoxicity is under investigation. In this study, using cell-based models, we show that poly-proline-arginine DPR (poly-PR), the most neurotoxic DPR in vitro, binds to adenosine deaminase acting on RNA (ADAR)1p110 and ADAR2 and inhibits their RNA editing activity. We further show that poly-PR impairs cellular stress response that is mediated by ADAR1p110. These results together suggest that the poly-PR-mediated inhibition of the ADAR activity contributes to C9-ALS/FTD-linked neurotoxicity.
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Affiliation(s)
- Hiroaki Suzuki
- Department of Pharmacology, School of Medicine, Tokyo Medical University, Tokyo, Japan
| | - Masaaki Matsuoka
- Department of Pharmacology, School of Medicine, Tokyo Medical University, Tokyo, Japan
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3
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Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
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Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
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4
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Costa Cruz PH, Kato Y, Nakahama T, Shibuya T, Kawahara Y. A comparative analysis of ADAR mutant mice reveals site-specific regulation of RNA editing. RNA (NEW YORK, N.Y.) 2020; 26:454-469. [PMID: 31941663 PMCID: PMC7075269 DOI: 10.1261/rna.072728.119] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/09/2020] [Indexed: 05/03/2023]
Abstract
Adenosine-to-inosine RNA editing is an essential post-transcriptional modification catalyzed by adenosine deaminase acting on RNA (ADAR)1 and ADAR2 in mammals. For numerous sites in coding sequences (CDS) and microRNAs, editing is highly conserved and has significant biological consequences, for example, by altering amino acid residues and target recognition. However, no comprehensive and quantitative studies have been undertaken to determine how specific ADARs contribute to conserved sites in vivo. Here, we amplified each RNA region with editing site(s) separately and combined these for deep sequencing. Then, we compared the editing ratios of all sites that were conserved in CDS and microRNAs in the cerebral cortex and spleen of wild-type mice, Adar1E861A/E861AIfih-/- mice expressing inactive ADAR1 (Adar1 KI) and Adar2-/-Gria2R/R (Adar2 KO) mice. We found that most of the sites showed a preference for one ADAR. In contrast, some sites, such as miR-3099-3p, showed no ADAR preference. In addition, we found that the editing ratio for several sites, such as DACT3 R/G, was up-regulated in either Adar mutant mouse strain, whereas a coordinated interplay between ADAR1 and ADAR2 was required for the efficient editing of specific sites, such as the 5-HT2CR B site. We further created double mutant Adar1 KI Adar2 KO mice and observed viable and fertile animals with the complete absence of editing, demonstrating that ADAR1 and ADAR2 are the sole enzymes responsible for all editing sites in vivo. Collectively, these findings indicate that editing is regulated in a site-specific manner by the different interplay between ADAR1 and ADAR2.
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Affiliation(s)
- Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
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5
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Jinnah H, Ulbricht RJ. Using mouse models to unlock the secrets of non-synonymous RNA editing. Methods 2018; 156:40-45. [PMID: 30827465 DOI: 10.1016/j.ymeth.2018.10.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/05/2018] [Accepted: 10/22/2018] [Indexed: 11/26/2022] Open
Abstract
The deamination of adenosine to inosine by RNA editing is a widespread post-transcriptional process that expands genetic diversity. Selective substitution of inosine for adenosine in pre-mRNA transcripts can alter splicing, mRNA stability, and the amino acid sequence of the encoded protein. The functional consequences of RNA editing-dependent amino acid substitution are known for only a handful of RNA editing substrates. Many of these studies began in heterologous mammalian expression systems; however, the gold-standard for determining the functional significance of transcript-specific re-coding A-to-I editing events is the generation of a mouse model that expresses only one RNA editing-dependent isoform. The frequency of site-specific RNA editing varies spatially, temporally, and in some diseases, therefore, determining the profile of RNA editing frequency is also an important element of research. Here we review the strengths and weaknesses of existing mouse models for the study of RNA editing, as well as methods for quantifying RNA editing frequencies in vivo. Importantly, we highlight opportunities for future RNA editing studies in mice, projecting that improvements in genome editing and high-throughput sequencing technologies will allow the field to excel in coming years.
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Affiliation(s)
- Hussain Jinnah
- Vanderbilt University, Department of Pharmacology, 8140 Medical Research Building 3, Nashville, TN 37240-1104, United States.
| | - Randi J Ulbricht
- Missouri State University, Department of Biomedical Sciences, 901 South National Avenue, Springfield, MO 65897, United States.
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6
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Sagredo EA, Blanco A, Sagredo AI, Pérez P, Sepúlveda-Hermosilla G, Morales F, Müller B, Verdugo R, Marcelain K, Harismendy O, Armisén R. ADAR1-mediated RNA-editing of 3'UTRs in breast cancer. Biol Res 2018; 51:36. [PMID: 30290838 PMCID: PMC6172785 DOI: 10.1186/s40659-018-0185-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/09/2018] [Indexed: 12/22/2022] Open
Abstract
Background Whole transcriptome RNA variant analyses have shown that adenosine deaminases acting on RNA (ADAR) enzymes modify a large proportion of cellular RNAs, contributing to transcriptome diversity and cancer evolution. Despite the advances in the understanding of ADAR function in breast cancer, ADAR RNA editing functional consequences are not fully addressed. Results We characterized A to G(I) mRNA editing in 81 breast cell lines, showing increased editing at 3′UTR and exonic regions in breast cancer cells compared to immortalized non-malignant cell lines. In addition, tumors from the BRCA TCGA cohort show a 24% increase in editing over normal breast samples when looking at 571 well-characterized UTRs targeted by ADAR1. Basal-like subtype breast cancer patients with high level of ADAR1 mRNA expression shows a worse clinical outcome and increased editing in their 3′UTRs. Interestingly, editing was particularly increased in the 3′UTRs of ATM, GINS4 and POLH transcripts in tumors, which correlated with their mRNA expression. We confirmed the role of ADAR1 in this regulation using a shRNA in a breast cancer cell line (ZR-75-1). Conclusions Altogether, these results revealed a significant association between the mRNA editing in genes related to cancer-relevant pathways and clinical outcomes, suggesting an important role of ADAR1 expression and function in breast cancer. Electronic supplementary material The online version of this article (10.1186/s40659-018-0185-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eduardo A Sagredo
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile.,Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alejandro Blanco
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile.,Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alfredo I Sagredo
- Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Paola Pérez
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile
| | - Gonzalo Sepúlveda-Hermosilla
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile
| | - Fernanda Morales
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile.,Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Bettina Müller
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Avenida Profesor Zañartu 1010, Santiago, Chile.,Grupo Oncológico Cooperativo Chileno de Investigación GOCCHI, Santiago, Chile
| | - Ricardo Verdugo
- Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Katherine Marcelain
- Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Olivier Harismendy
- Moores Cancer Center and Division of Biomedical Informatics, Department of Medicine, School of Medicine, University of California, San Diego, CA, USA.
| | - Ricardo Armisén
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile. .,Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile. .,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile. .,Grupo Oncológico Cooperativo Chileno de Investigación GOCCHI, Santiago, Chile.
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7
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Roberts JT, Patterson DG, King VM, Amin SV, Polska CJ, Houserova D, Crucello A, Barnhill EC, Miller MM, Sherman TD, Borchert GM. ADAR Mediated RNA Editing Modulates MicroRNA Targeting in Human Breast Cancer. Processes (Basel) 2018; 6. [PMID: 30197877 PMCID: PMC6128407 DOI: 10.3390/pr6050042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA editing by RNA specific adenosine deaminase acting on RNA (ADAR) is increasingly being found to alter microRNA (miRNA) regulation. Editing of miRNA transcripts can affect their processing, as well as which messenger RNAs (mRNAs) they target. Further, editing of target mRNAs can also affect their complementarity to miRNAs. Notably, ADAR editing is often increased in malignancy with the effect of these RNA changes being largely unclear. In addition, numerous reports have now identified an array of miRNAs that directly contribute to various malignancies although the majority of their targets remain largely undefined. Here we propose that modulating the targets of miRNAs via mRNA editing is a frequent occurrence in cancer and an underappreciated participant in pathology. In order to more accurately characterize the relationship between these two regulatory processes, this study examined RNA editing events within mRNA sequences of two breast cancer cell lines (MCF-7 and MDA-MB-231) and determined whether or not these edits could modulate miRNA associations. Computational analyses of RNA-Seq data from these two cell lines identified over 50,000 recurrent editing sites within human mRNAs, and many of these were located in 3’ untranslated regions (UTRs). When these locations were screened against the list of currently-annotated miRNAs we discovered that editing caused a subset (~9%) to have significant alterations to mRNA complementarity. One miRNA in particular, miR-140–3p, is known to be misexpressed in many breast cancers, and we found that mRNA editing allowed this miRNA to directly target the apoptosis inducing gene DFFA in MCF-7, but not in MDA-MB-231 cells. As these two cell lines are known to have distinct characteristics in terms of morphology, invasiveness and physiological responses, we hypothesized that the differential RNA editing of DFFA in these two cell lines could contribute to their phenotypic differences. Indeed, we confirmed through western blotting that inhibiting miR-140–3p increases expression of the DFFA protein product in MCF-7, but not MDA-MB-231, and further that inhibition of miR-140–3p also increases cellular growth in MCF-7, but not MDA-MB-231. Broadly, these results suggest that the creation of miRNA targets may be an underappreciated function of ADAR and may help further elucidate the role of RNA editing in tumor pathogenicity.
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Affiliation(s)
- Justin T Roberts
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Dillon G Patterson
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Valeria M King
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Shivam V Amin
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Caroline J Polska
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Dominika Houserova
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA;
| | - Aline Crucello
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Emmaline C Barnhill
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Molly M Miller
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Timothy D Sherman
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Glen M Borchert
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA;
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8
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Uchida H, Matsumura S, Okada S, Suzuki T, Minami T, Ito S. RNA editing enzyme ADAR2 is a mediator of neuropathic pain after peripheral nerve injury. FASEB J 2017; 31:1847-1855. [PMID: 28126736 DOI: 10.1096/fj.201600950r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/03/2017] [Indexed: 12/15/2022]
Abstract
Transcriptional and post-translational regulations are important in peripheral nerve injury-induced neuropathic pain, but little is known about the role of post-transcriptional modification. Our objective was to determine the possible effect of adenosine deaminase acting on RNA (ADAR) enzymes, which catalyze post-transcriptional RNA editing, in tactile allodynia, a hallmark of neuropathic pain. Seven days after L5 spinal nerve transection (SNT) in adult mice, we found an increase in ADAR2 expression and a decrease in ADAR3 expression in the injured, but not in the uninjured, dorsal root ganglions (DRGs). These changes were accompanied by elevated levels of editing at the D site of the serotonin (5-hydroxytryptamine) 2C receptor (5-HT2CR), at the I/V site of coatomer protein complex subunit α (COPA), and at the R/G site of AMPA receptor subunit GluA2 in the injured DRG. Compared to Adar2+/+/Gria2R/R littermate controls, Adar2-/-/Gria2R/R mice completely lacked the increased editing of 5-HT2CR, COPA, and GluA2 transcripts in the injured DRG and showed attenuated tactile allodynia after SNT. Furthermore, the antidepressant fluoxetine inhibited neuropathic allodynia after injury and reduced the COPA I/V site editing in the injured DRG. These findings suggest that ADAR2 is a mediator of injury-induced tactile allodynia and thus a potential therapeutic target for the treatment of neuropathic pain.-Uchida, H., Matsumura, S., Okada, S., Suzuki, T., Minami, T., Ito, S. RNA editing enzyme ADAR2 is a mediator of neuropathic pain after peripheral nerve injury.
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Affiliation(s)
- Hitoshi Uchida
- Department of Medical Chemistry, Kansai Medical University, Osaka, Japan
| | - Shinji Matsumura
- Department of Medical Chemistry, Kansai Medical University, Osaka, Japan
| | - Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan; and
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan; and
| | - Toshiaki Minami
- Department of Anesthesiology, Osaka Medical College, Osaka, Japan
| | - Seiji Ito
- Department of Medical Chemistry, Kansai Medical University, Osaka, Japan;
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9
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Mazloomian A, Meyer IM. Genome-wide identification and characterization of tissue-specific RNA editing events in D. melanogaster and their potential role in regulating alternative splicing. RNA Biol 2016; 12:1391-401. [PMID: 26512413 PMCID: PMC4829317 DOI: 10.1080/15476286.2015.1107703] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RNA editing is a widespread mechanism that plays a crucial role in diversifying gene products. Its abundance and importance in regulating cellular processes were revealed using new sequencing technologies. The majority of these editing events, however, cannot be associated with regulatory mechanisms. We use tissue-specific high-throughput libraries of D. melanogaster to study RNA editing. We introduce an analysis pipeline that utilises large input data and explicitly captures ADAR's requirement for double-stranded regions. It combines probabilistic and deterministic filters and can identify RNA editing events with a low estimated false positive rate. Analyzing ten different tissue types, we predict 2879 editing sites and provide their detailed characterization. Our analysis pipeline accurately distinguishes genuine editing sites from SNPs and sequencing and mapping artifacts. Our editing sites are 3 times more likely to occur in exons with multiple splicing acceptor/donor sites than in exons with unique splice sites (p-value < 2.10−15). Furthermore, we identify 244 edited regions where RNA editing and alternative splicing are likely to influence each other. For 96 out of these 244 regions, we find evolutionary evidence for conserved RNA secondary-structures near splice sites suggesting a potential regulatory mechanism where RNA editing may alter splicing patterns via changes in local RNA structure.
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Affiliation(s)
- Alborz Mazloomian
- a Centre for High-Throughput Biology; Department of Computer Science and Department of Medical Genetics ; University of British Columbia ; Vancouver ; BC , Canada
| | - Irmtraud M Meyer
- a Centre for High-Throughput Biology; Department of Computer Science and Department of Medical Genetics ; University of British Columbia ; Vancouver ; BC , Canada
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10
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Germain A, Hanson MR, Bentolila S. High-throughput quantification of chloroplast RNA editing extent using multiplex RT-PCR mass spectrometry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:546-554. [PMID: 26032222 DOI: 10.1111/tpj.12892] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/14/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
RNA editing in plants, animals, and humans modifies genomically encoded cytidine or adenosine nucleotides to uridine or inosine, respectively, in mRNAs. We customized the MassARRAY System (Sequenom Inc., San Diego, CA, USA, www.sequenom.com) to assay multiplex PCR-amplified single-stranded cDNAs and easily analyse and display the captured data. By using appropriate oligonucleotide probes, the method can be tailored to any organism and gene where RNA editing occurs. Editing extent of up to 40 different nucleotides in each of either 94 or 382 different samples (3760 or 15 280 editing targets, respectively) can be examined by assaying a single plate and by performing one repetition. We have established this mass spectrometric method as a dependable, cost-effective and time-saving technique to examine the RNA editing efficiency at 37 Arabidopsis thaliana chloroplast editing sites at a high level of multiplexing. The high-throughput editing assay, named Multiplex RT-PCR Mass Spectrometry (MRMS), is ideal for large-scale experiments such as identifying population variation, examining tissue-specific changes in editing extent, or screening a mutant or transgenic collection. Moreover, the required amount of starting material is so low that RNA from fewer than 50 cells can be examined without amplification. We demonstrate the use of the method to identify natural variation in editing extent of chloroplast C targets in a collection of Arabidopsis accessions.
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Affiliation(s)
- Arnaud Germain
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, 14853, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, 14853, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, 14853, USA
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11
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Frésard L, Leroux S, Roux PF, Klopp C, Fabre S, Esquerré D, Dehais P, Djari A, Gourichon D, Lagarrigue S, Pitel F. Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates. PLoS One 2015; 10:e0126776. [PMID: 26024316 PMCID: PMC4449034 DOI: 10.1371/journal.pone.0126776] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 04/07/2015] [Indexed: 12/15/2022] Open
Abstract
RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome.
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Affiliation(s)
- Laure Frésard
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Sophie Leroux
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Pierre-François Roux
- Agrocampus Ouest, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France
- INRA, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France
| | - Christophe Klopp
- INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Stéphane Fabre
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Diane Esquerré
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- INRA, GeT-PlaGe Genotoul, Castanet-Tolosan, France
| | - Patrice Dehais
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Anis Djari
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - David Gourichon
- INRA, Pôle d'Expérimentation Avicole de Tours, Nouzilly, France
| | - Sandrine Lagarrigue
- Agrocampus Ouest, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France
- INRA, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France
| | - Frédérique Pitel
- INRA, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
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12
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Difference in microRNA expression and editing profile of lung tissues from different pig breeds related to immune responses to HP-PRRSV. Sci Rep 2015; 5:9549. [PMID: 25856272 PMCID: PMC5381705 DOI: 10.1038/srep09549] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/26/2015] [Indexed: 12/21/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is one of the most devastating diseases for the pig industry. Our goal was to identify microRNAs involved in the host immune response to PRRS. We generated microRNA expression profiles of lung tissues from Tongcheng or Landrace pigs infected with a highly pathogenic PRRS virus (PRRSV) at 3, 5, 7 dpi (day post infection) and control individuals from these two breeds. Our data showed that 278 known and 294 novel microRNAs were expressed in these combined microRNA transcriptomes. Compared with control individuals, almost half of the known microRNAs (116 in Tongcheng and 153 in Landrace) showed significantly differential expression (DEmiRNAs) at least once. The numbers of down-regulated DEmiRNAs were larger than the corresponding number of up-regulated DEmiRNAs in both breeds. Interestingly, miR-2320-5p, which was predicted to bind to conserved sequences of the PRRSV genome, was down-regulated significantly at 3 dpi after PRRSV infection in both breeds. In addition, PRRSV infection induced a significant increase of microRNA editing level in both breeds. Our results provide novel insight into the role of microRNA in response to PRRSV infection in vivo, which will aid the research for developing novel therapies against PRRSV.
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13
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Yamashita T, Kwak S. The molecular link between inefficient GluA2 Q/R site-RNA editing and TDP-43 pathology in motor neurons of sporadic amyotrophic lateral sclerosis patients. Brain Res 2014; 1584:28-38. [DOI: 10.1016/j.brainres.2013.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 12/04/2013] [Accepted: 12/07/2013] [Indexed: 12/12/2022]
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14
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Wu P, Zhang H, Lin W, Hao Y, Ren L, Zhang C, Li N, Wei H, Jiang Y, He F. Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver. J Proteome Res 2014; 13:2409-19. [PMID: 24717071 DOI: 10.1021/pr4012206] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Comprehensively identifying gene expression in both transcriptomic and proteomic levels of one tissue is a prerequisite for a deeper understanding of its biological functions. Alternative splicing and RNA editing, two main forms of transcriptional processing, play important roles in transcriptome and proteome diversity and result in multiple isoforms for one gene, which are hard to identify by mass spectrometry (MS)-based proteomics approach due to the relative lack of isoform information in standard protein databases. In our study, we employed MS and RNA-Seq in parallel into mouse liver tissue and captured a considerable catalogue of both transcripts and proteins that, respectively, covered 60 and 34% of protein-coding genes in Ensembl. We then developed a bioinformatics workflow for building a customized protein database that for the first time included new splicing-derived peptides and RNA-editing-caused peptide variants, allowing us to more completely identify protein isoforms. Using this experimentally determined database, we totally identified 150 peptides not present in standard biological databases at false discovery rate of <1%, corresponding to 72 novel splicing isoforms, 43 new genetic regions, and 15 RNA-editing sites. Of these, 11 randomly selected novel events passed experimental verification by PCR and Sanger sequencing. New discoveries of gene products with high confidence in two omics levels demonstrated the robustness and effectiveness of our approach and its potential application into improve genome annotation. All the MS data have been deposited to the iProx ( http://ww.iprox.org ) with the identifier IPX00003601.
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Affiliation(s)
- Peng Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , 33 Life Science Park Road, Beijing 102206, China
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15
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Sakurai M, Ueda H, Yano T, Okada S, Terajima H, Mitsuyama T, Toyoda A, Fujiyama A, Kawabata H, Suzuki T. A biochemical landscape of A-to-I RNA editing in the human brain transcriptome. Genome Res 2014; 24:522-34. [PMID: 24407955 PMCID: PMC3941116 DOI: 10.1101/gr.162537.113] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inosine is an abundant RNA modification in the human transcriptome and is essential for many biological processes in modulating gene expression at the post-transcriptional level. Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosines to inosines (A-to-I editing) in double-stranded regions. We previously established a biochemical method called "inosine chemical erasing" (ICE) to directly identify inosines on RNA strands with high reliability. Here, we have applied the ICE method combined with deep sequencing (ICE-seq) to conduct an unbiased genome-wide screening of A-to-I editing sites in the transcriptome of human adult brain. Taken together with the sites identified by the conventional ICE method, we mapped 19,791 novel sites and newly found 1258 edited mRNAs, including 66 novel sites in coding regions, 41 of which cause altered amino acid assignment. ICE-seq detected novel editing sites in various repeat elements as well as in short hairpins. Gene ontology analysis revealed that these edited mRNAs are associated with transcription, energy metabolism, and neurological disorders, providing new insights into various aspects of human brain functions.
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Affiliation(s)
- Masayuki Sakurai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
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16
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Pinto Y, Cohen HY, Levanon EY. Mammalian conserved ADAR targets comprise only a small fragment of the human editosome. Genome Biol 2014; 15:R5. [PMID: 24393560 PMCID: PMC4053846 DOI: 10.1186/gb-2014-15-1-r5] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/07/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND ADAR proteins are among the most extensively studied RNA binding proteins. They bind to their target and deaminate specific adenosines to inosines. ADAR activity is essential, and the editing of a subset of their targets is critical for viability. Recently, a huge number of novel ADAR targets were detected by analyzing next generation sequencing data. Most of these novel editing sites are located in lineage-specific genomic repeats, probably a result of overactivity of editing enzymes, thus masking the functional sites. In this study we aim to identify the set of mammalian conserved ADAR targets. RESULTS We used RNA sequencing data from human, mouse, rat, cow, opossum, and platypus to define the conserved mammalian set of ADAR targets. We found that the conserved mammalian editing sites are surprisingly small in number and have unique characteristics that distinguish them from non-conserved ones. The sites that constitute the set have a distinct genomic distribution, tend to be located in genes encoding neurotransmitter receptors or other synapse related proteins, and have higher editing and expression levels. We also found a high consistency of editing levels of this set within mice strains and between human and mouse. Tight regulation of editing in these sites across strains and species implies their functional importance. CONCLUSIONS Despite the discovery of numerous editing targets, only a small number of them are conserved within mammalian evolution. These sites are extremely highly conserved and exhibit unique features, such as tight regulation, and probably play a pivotal role in mammalian biology.
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17
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Frańska M. Inosine octamer stabilized by alkali earth metal cations - as studied by electrospray ionization mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:249-253. [PMID: 24892295 DOI: 10.1255/ejms.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
By using electrospray ionization mass spectrometry, inosine was found to be able to form an octamer stabilized by alkali earth metal cation, namely Ca(2+), Sr(2+) and Ba(2+), of which the most stable is that stabilized by Ca(2+) (ion [I8+Ca](2+)). It was established that 9-methylhypoxanthine (M) did not form an analogical octamer, since ion [M8+Ca](2+) was not detected. On the other hand, 9-methylhypoxanthine can form "mixed" octamers together with inosine (ions [InMm+Ca](2+), n + m = 8, were detected).
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Affiliation(s)
- Magdalena Frańska
- Poznań University of Technology, Institute of Chemistry, Piotrowo 3, 60-965 Poznań, Poland.
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18
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Picardi E, Gallo A, Galeano F, Tomaselli S, Pesole G. A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue. PLoS One 2012; 7:e44184. [PMID: 22957051 PMCID: PMC3434223 DOI: 10.1371/journal.pone.0044184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/30/2012] [Indexed: 01/30/2023] Open
Abstract
RNA editing is a post-transcriptional process occurring in a wide range of organisms. In human brain, the A-to-I RNA editing, in which individual adenosine (A) bases in pre-mRNA are modified to yield inosine (I), is the most frequent event. Modulating gene expression, RNA editing is essential for cellular homeostasis. Indeed, its deregulation has been linked to several neurological and neurodegenerative diseases. To date, many RNA editing sites have been identified by next generation sequencing technologies employing massive transcriptome sequencing together with whole genome or exome sequencing. While genome and transcriptome reads are not always available for single individuals, RNA-Seq data are widespread through public databases and represent a relevant source of yet unexplored RNA editing sites. In this context, we propose a simple computational strategy to identify genomic positions enriched in novel hypothetical RNA editing events by means of a new two-steps mapping procedure requiring only RNA-Seq data and no a priori knowledge of RNA editing characteristics and genomic reads. We assessed the suitability of our procedure by confirming A-to-I candidates using conventional Sanger sequencing and performing RNA-Seq as well as whole exome sequencing of human spinal cord tissue from a single individual.
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Affiliation(s)
- Ernesto Picardi
- Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Università di Bari, Bari, Italy
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, Ospedale Pediatrico “Bambino Gesù”, IRCCS, Rome, Italy
| | - Federica Galeano
- RNA Editing Laboratory, Oncohaematology Department, Ospedale Pediatrico “Bambino Gesù”, IRCCS, Rome, Italy
| | - Sara Tomaselli
- RNA Editing Laboratory, Oncohaematology Department, Ospedale Pediatrico “Bambino Gesù”, IRCCS, Rome, Italy
| | - Graziano Pesole
- Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Università di Bari, Bari, Italy
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy
- * E-mail:
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Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J. Quantitative biology of single neurons. J R Soc Interface 2012; 9:3165-83. [PMID: 22915636 PMCID: PMC3481569 DOI: 10.1098/rsif.2012.0417] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible.
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Affiliation(s)
- James Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 36th and Hamilton Walk, Philadelphia, PA 19104, USA.
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20
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Zhu H, Urban DJ, Blashka J, McPheeters MT, Kroeze WK, Mieczkowski P, Overholser JC, Jurjus GJ, Dieter L, Mahajan GJ, Rajkowska G, Wang Z, Sullivan PF, Stockmeier CA, Roth BL. Quantitative analysis of focused a-to-I RNA editing sites by ultra-high-throughput sequencing in psychiatric disorders. PLoS One 2012; 7:e43227. [PMID: 22912834 PMCID: PMC3422315 DOI: 10.1371/journal.pone.0043227] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/18/2012] [Indexed: 12/01/2022] Open
Abstract
A-to-I RNA editing is a post-transcriptional modification of single nucleotides in RNA by adenosine deamination, which thereby diversifies the gene products encoded in the genome. Thousands of potential RNA editing sites have been identified by recent studies (e.g. see Li et al, Science 2009); however, only a handful of these sites have been independently confirmed. Here, we systematically and quantitatively examined 109 putative coding region A-to-I RNA editing sites in three sets of normal human brain samples by ultra-high-throughput sequencing (uHTS). Forty of 109 putative sites, including 25 previously confirmed sites, were validated as truly edited in our brain samples, suggesting an overestimation of A-to-I RNA editing in these putative sites by Li et al (2009). To evaluate RNA editing in human disease, we analyzed 29 of the confirmed sites in subjects with major depressive disorder and schizophrenia using uHTS. In striking contrast to many prior studies, we did not find significant alterations in the frequency of RNA editing at any of the editing sites in samples from these patients, including within the 5HT2C serotonin receptor (HTR2C). Our results indicate that uHTS is a fast, quantitative and high-throughput method to assess RNA editing in human physiology and disease and that many prior studies of RNA editing may overestimate both the extent and disease-related variability of RNA editing at the sites we examined in the human brain.
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Affiliation(s)
- Hu Zhu
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Daniel J. Urban
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Jared Blashka
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Matthew T. McPheeters
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Wesley K. Kroeze
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Piotr Mieczkowski
- Department of Genetics, School of Medicine, Chapel Hill, North Carolina, United States of America
| | - James C. Overholser
- Department of Psychology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - George J. Jurjus
- Department of Psychiatry, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Psychiatry, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, United States of America
| | - Lesa Dieter
- Department of Psychology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gouri J. Mahajan
- Center for Psychiatric Neuroscience, Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Grazyna Rajkowska
- Center for Psychiatric Neuroscience, Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Zefeng Wang
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
| | - Patrick F. Sullivan
- Department of Genetics, School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Craig A. Stockmeier
- Department of Psychiatry, Case Western Reserve University, Cleveland, Ohio, United States of America
- Center for Psychiatric Neuroscience, Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, North Carolina, United States of America
- * E-mail:
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21
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Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell 2012; 149:1635-46. [PMID: 22608085 DOI: 10.1016/j.cell.2012.05.003] [Citation(s) in RCA: 2876] [Impact Index Per Article: 239.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/15/2012] [Accepted: 03/27/2012] [Indexed: 02/07/2023]
Abstract
Methylation of the N(6) position of adenosine (m(6)A) is a posttranscriptional modification of RNA with poorly understood prevalence and physiological relevance. The recent discovery that FTO, an obesity risk gene, encodes an m(6)A demethylase implicates m(6)A as an important regulator of physiological processes. Here, we present a method for transcriptome-wide m(6)A localization, which combines m(6)A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m(6)A, indicating that m(6)A is a common base modification of mRNA. The m(6)A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m(6)A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m(6)A residues and microRNA-binding sites within 3' UTRs. These findings provide a resource for identifying transcripts that are substrates for adenosine methylation and reveal insights into the epigenetic regulation of the mammalian transcriptome.
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22
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Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 2012; 30:253-60. [PMID: 22327324 DOI: 10.1038/nbt.2122] [Citation(s) in RCA: 400] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/17/2012] [Indexed: 01/08/2023]
Abstract
RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual. We identified 22,688 RNA editing events in noncoding genes and introns, untranslated regions and coding sequences of protein-coding genes. Most changes (∼93%) converted A to I(G), consistent with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). We also found evidence of other types of nucleotide changes; however, these were validated at lower rates. We found 44 editing sites in microRNAs (miRNAs), suggesting a potential link between RNA editing and miRNA-mediated regulation. Our approach facilitates large-scale studies to profile and compare editomes across a wide range of samples.
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23
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Base modification RNA editing: information recoding on the fly. Semin Cell Dev Biol 2011; 23:243. [PMID: 22193702 DOI: 10.1016/j.semcdb.2011.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Steele EJ, Lindley RA, Weiller GW. Somatic hypermutation and the discovery of A-to-I RNA editing sites? Biochem Biophys Res Commun 2011; 414:443. [DOI: 10.1016/j.bbrc.2011.09.111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 09/22/2011] [Indexed: 11/28/2022]
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